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vep-software [2017/09/28 11:57]
aorth [Variant Effect Predictor(VEP)]
vep-software [2019/08/11 18:41]
aorth
Line 5: Line 5:
 ===== Information ===== ===== Information =====
  
-  * Latest Version: 87+  * Latest Version: 92.1
   * Added: February, 2017   * Added: February, 2017
-  * Link: http://www.ensembl.org/info/docs/tools/vep/index.html +  * Updated: April, 2018 
-  * Annotations: ''/export/data/bio/vep/''+  * Link: https://github.com/Ensembl/ensembl-vep 
 +  * Annotations: ''/export/apps/vep/92.1/cache''
  
 ===== Usage ===== ===== Usage =====
Line 15: Line 16:
 <code>$ module avail vep</code> <code>$ module avail vep</code>
  
-===== Installation ====== +Load one version into your environment and run it: 
-Notes from the sysadmin during installation:+<code>$ module load vep/92.1 
 +$ vep --cache /export/apps/vep/92.1/cache 
 +</code>
  
-<code> +**N.B.** The VEP cache is installed in ''/export/apps/vep/92.1/cache'', so make sure to specify this when working with VEPContact Alan or Jean-Baka if you need more databases installed.
-- install vep-script +
-$ sudo mkdir -p /export/apps/vep/87/ +
-$ sudo chown -R joguya:joguya /export/apps/vep/87/ +
-$ cd scripts/variant_effect_predictor +
-$ module load perl/5.22.3 +
-$ scl enable devtoolset-3 bash +
-$ cpanm File::Copy::Recursive Archive::Extract LWP::Simple LWP::Protocol::https CGI +
-$ module load htslib/1.3.2 +
-$ mkdir /export/apps/vep/87/cache +
-$ perl INSTALL.pl --DESTDIR /export/apps/vep/87 --NO_HTSLIB  +
-$ PERL5LIB=$PERL5LIB:/export/apps/vep/87 perl INSTALL.pl --DESTDIR /export/apps/vep/87 --NO_HTSLIB +
-$ cp *.pl *.vcf /export/apps/vep/87/ +
-$ sudo chown -R root:root /export/apps/vep/87/+
  
-- download cattle annotation data to /export/data/ for use by VEP in /export/data/bio +===== Installation ====== 
-$ sudo mkdir /export/data/bio/vep +Notes from the sysadmin during installation:
-$ sudo chown joguya:joguya /export/data/bio/vep +
-$ PERL5LIB=$PERL5LIB:/export/apps/vep/87 perl INSTALL.pl --DESTDIR /export/apps/vep/87 --CACHEDIR /export/data/bio/vep --NO_HTSLIB +
-$ sudo chown -R root:root /export/data/bio/vep +
-</code>+
  
 +<code>$ cd /tmp
 +$ curl -L -O https://github.com/Ensembl/ensembl-vep/archive/release/92.1.zip
 +$ unzip 92.1.zip
 +$ sudo yum install perl-DBI perl-DBD-mysql perl-JSON perl-perlIO-gzip
 +$ module load htslib/1.6
 +$ cd ensembl-vep-release-92.1
 +$ cpanm -l . Set::IntervalTree
 +$ mkdir cache
 +$ PERL5LIB=lib/perl5 perl INSTALL.pl --NO_HTSLIB --CACHEDIR cache
 +$ sudo mkdir -p /export/apps/vep/92.1
 +$ sudo cp -r * /export/apps/vep/92.1</code>
vep-software.txt · Last modified: 2019/08/11 18:41 by aorth